請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/23898
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 邱繼輝(Kay-Hooi Khoo) | |
dc.contributor.author | Ying-Che Chang | en |
dc.contributor.author | 張瑩徹 | zh_TW |
dc.date.accessioned | 2021-06-08T05:12:13Z | - |
dc.date.copyright | 2011-08-22 | |
dc.date.issued | 2011 | |
dc.date.submitted | 2011-08-02 | |
dc.identifier.citation | [1] Tonks, N. K., Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol 2006, 7, 833-846.
[2] Mustelin, T., Vang, T., Bottini, N., Protein tyrosine phosphatases and the immune response. Nat Rev Immunol 2005, 5, 43-57. [3] Tonks, N. K., Diltz, C. D., Fischer, E. H., Purification of the major protein-tyrosine-phosphatases of human placenta. J Biol Chem 1988, 263, 6722-6730. [4] Czernilofsky, A. P., Levinson, A. D., Varmus, H. E., Bishop, J. M., et al., Nucleotide sequence of an avian sarcoma virus oncogene (src) and proposed amino acid sequence for gene product. Nature 1980, 287, 198-203. [5] Eckhart, W., Hutchinson, M. A., Hunter, T., An activity phosphorylating tyrosine in polyoma T antigen immunoprecipitates. Cell 1979, 18, 925-933. [6] Alonso, A., Sasin, J., Bottini, N., Friedberg, I., et al., Protein tyrosine phosphatases in the human genome. Cell 2004, 117, 699-711. [7] Ostman, A., Hellberg, C., Bohmer, F. D., Protein-tyrosine phosphatases and cancer. Nat Rev Cancer 2006, 6, 307-320. [8] Julien, S. G., Dube, N., Hardy, S., Tremblay, M. L., Inside the human cancer tyrosine phosphatome. Nat Rev Cancer, 11, 35-49. [9] Peters, G. H., Frimurer, T. M., Olsen, O. H., Electrostatic evaluation of the signature motif (H/V)CX5R(S/T) in protein-tyrosine phosphatases. Biochemistry 1998, 37, 5383-5393. [10] Guan, K. L., Dixon, J. E., Evidence for protein-tyrosine-phosphatase catalysis proceeding via a cysteine-phosphate intermediate. J Biol Chem 1991, 266, 17026-17030. [11] Blanchetot, C., Tertoolen, L. G., Overvoorde, J., den Hertog, J., Intra- and intermolecular interactions between intracellular domains of receptor protein-tyrosine phosphatases. J Biol Chem 2002, 277, 47263-47269. [12] Jiang, G., den Hertog, J., Hunter, T., Receptor-like protein tyrosine phosphatase alpha homodimerizes on the cell surface. Mol Cell Biol 2000, 20, 5917-5929. [13] Felberg, J., Johnson, P., Characterization of recombinant CD45 cytoplasmic domain proteins. Evidence for intramolecular and intermolecular interactions. J Biol Chem 1998, 273, 17839-17845. [14] Streuli, M., Krueger, N. X., Thai, T., Tang, M., Saito, H., Distinct functional roles of the two intracellular phosphatase like domains of the receptor-linked protein tyrosine phosphatases LCA and LAR. EMBO J 1990, 9, 2399-2407. [15] Chagnon, M. J., Uetani, N., Tremblay, M. L., Functional significance of the LAR receptor protein tyrosine phosphatase family in development and diseases. Biochem Cell Biol 2004, 82, 664-675. [16] Andersen, J. N., Jansen, P. G., Echwald, S. M., Mortensen, O. H., et al., A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage. FASEB J 2004, 18, 8-30. [17] Liang, F., Kumar, S., Zhang, Z. Y., Proteomic approaches to studying protein tyrosine phosphatases. Mol Biosyst 2007, 3, 308-316. [18] Flint, A. J., Tiganis, T., Barford, D., Tonks, N. K., Development of 'substrate-trapping' mutants to identify physiological substrates of protein tyrosine phosphatases. Proc Natl Acad Sci U S A 1997, 94, 1680-1685. [19] Blanchetot, C., Chagnon, M., Dube, N., Halle, M., Tremblay, M. L., Substrate-trapping techniques in the identification of cellular PTP targets. Methods 2005, 35, 44-53. [20] Fukada, M., Kawachi, H., Fujikawa, A., Noda, M., Yeast substrate-trapping system for isolating substrates of protein tyrosine phosphatases: Isolation of substrates for protein tyrosine phosphatase receptor type z. Methods 2005, 35, 54-63. [21] Wu, J., Katrekar, A., Honigberg, L. A., Smith, A. M., et al., Identification of substrates of human protein-tyrosine phosphatase PTPN22. J Biol Chem 2006, 281, 11002-11010. [22] Kolli, S., Zito, C. I., Mossink, M. H., Wiemer, E. A., Bennett, A. M., The major vault protein is a novel substrate for the tyrosine phosphatase SHP-2 and scaffold protein in epidermal growth factor signaling. J Biol Chem 2004, 279, 29374-29385. [23] Andersen, J. N., Mortensen, O. H., Peters, G. H., Drake, P. G., et al., Structural and evolutionary relationships among protein tyrosine phosphatase domains. Mol Cell Biol 2001, 21, 7117-7136. [24] Zhang, Z. Y., Mechanistic studies on protein tyrosine phosphatases. Prog Nucleic Acid Res Mol Biol 2003, 73, 171-220. [25] Stuckey, J. A., Schubert, H. L., Fauman, E. B., Zhang, Z. Y., et al., Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate. Nature 1994, 370, 571-575. [26] Jia, Z., Barford, D., Flint, A. J., Tonks, N. K., Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B. Science 1995, 268, 1754-1758. [27] Sun, H., Charles, C. H., Lau, L. F., Tonks, N. K., MKP-1 (3CH134), an immediate early gene product, is a dual specificity phosphatase that dephosphorylates MAP kinase in vivo. Cell 1993, 75, 487-493. [28] Furukawa, T., Itoh, M., Krueger, N. X., Streuli, M., Saito, H., Specific interaction of the CD45 protein-tyrosine phosphatase with tyrosine-phosphorylated CD3 zeta chain. Proc Natl Acad Sci U S A 1994, 91, 10928-10932. [29] Zhang, Z. Y., Wu, L., The single sulfur to oxygen substitution in the active site nucleophile of the Yersinia protein-tyrosine phosphatase leads to substantial structural and functional perturbations. Biochemistry 1997, 36, 1362-1369. [30] Garton, A. J., Flint, A. J., Tonks, N. K., Identification of p130(cas) as a substrate for the cytosolic protein tyrosine phosphatase PTP-PEST. Mol Cell Biol 1996, 16, 6408-6418. [31] Agazie, Y. M., Hayman, M. J., Development of an efficient 'substrate-trapping' mutant of Src homology phosphotyrosine phosphatase 2 and identification of the epidermal growth factor receptor, Gab1, and three other proteins as target substrates. J Biol Chem 2003, 278, 13952-13958. [32] Xie, L., Zhang, Y. L., Zhang, Z. Y., Design and characterization of an improved protein tyrosine phosphatase substrate-trapping mutant. Biochemistry 2002, 41, 4032-4039. [33] Zhang, S. H., Liu, J., Kobayashi, R., Tonks, N. K., Identification of the cell cycle regulator VCP (p97/CDC48) as a substrate of the band 4.1-related protein-tyrosine phosphatase PTPH1. J Biol Chem 1999, 274, 17806-17812. [34] Kontaridis, M. I., Eminaga, S., Fornaro, M., Zito, C. I., et al., SHP-2 positively regulates myogenesis by coupling to the Rho GTPase signaling pathway. Mol Cell Biol 2004, 24, 5340-5352. [35] Romsicki, Y., Scapin, G., Beaulieu-Audy, V., Patel, S., et al., Functional characterization and crystal structure of the C215D mutant of protein-tyrosine phosphatase-1B. J Biol Chem 2003, 278, 29009-29015. [36] Schindelholz, B., Knirr, M., Warrior, R., Zinn, K., Regulation of CNS and motor axon guidance in Drosophila by the receptor tyrosine phosphatase DPTP52F. Development 2001, 128, 4371-4382. [37] Stoker, A. W., Receptor tyrosine phosphatases in axon growth and guidance. Curr Opin Neurobiol 2001, 11, 95-102. [38] Chen, F., Archambault, V., Kar, A., Lio, P., et al., Multiple protein phosphatases are required for mitosis in Drosophila. Curr Biol 2007, 17, 293-303. [39] Gilbert, M. M., Tipping, M., Veraksa, A., Moberg, K. H., A Screen for Conditional Growth Suppressor Genes Identifies the Drosophila Homolog of HD-PTP as a Regulator of the Oncoprotein Yorkie. Dev Cell, 20, 700-712. [40] Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., et al., The genome sequence of Drosophila melanogaster. Science 2000, 287, 2185-2195. [41] Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., et al., The sequence of the human genome. Science 2001, 291, 1304-1351. [42] Brogiolo, W., Stocker, H., Ikeya, T., Rintelen, F., et al., An evolutionarily conserved function of the Drosophila insulin receptor and insulin-like peptides in growth control. Curr Biol 2001, 11, 213-221. [43] Arbouzova, N. I., Zeidler, M. P., JAK/STAT signalling in Drosophila: insights into conserved regulatory and cellular functions. Development 2006, 133, 2605-2616. [44] Pandey, U. B., Nichols, C. D., Human disease models in Drosophila melanogaster and the role of the fly in therapeutic drug discovery. Pharmacol Rev, 63, 411-436. [45] Andersen, J. N., Del Vecchio, R. L., Kannan, N., Gergel, J., et al., Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources. Methods 2005, 35, 90-114. [46] Dube, N., Tremblay, M. L., Involvement of the small protein tyrosine phosphatases TC-PTP and PTP1B in signal transduction and diseases: from diabetes, obesity to cell cycle, and cancer. Biochim Biophys Acta 2005, 1754, 108-117. [47] Matthews, K. A., Kaufman, T. C., Gelbart, W. M., Research resources for Drosophila: the expanding universe. Nat Rev Genet 2005, 6, 179-193. [48] The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 2002, 30, 106-108. [49] Fischer, J. A., Giniger, E., Maniatis, T., Ptashne, M., GAL4 activates transcription in Drosophila. Nature 1988, 332, 853-856. [50] Elliott, D. A., Brand, A. H., The GAL4 system : a versatile system for the expression of genes. Methods Mol Biol 2008, 420, 79-95. [51] Rubin, G. M., Spradling, A. C., Genetic transformation of Drosophila with transposable element vectors. Science 1982, 218, 348-353. [52] Bachmann, A., Knust, E., The use of P-element transposons to generate transgenic flies. Methods Mol Biol 2008, 420, 61-77. [53] Xu, T., Rubin, G. M., Analysis of genetic mosaics in developing and adult Drosophila tissues. Development 1993, 117, 1223-1237. [54] Golic, K. G., Golic, M. M., Engineering the Drosophila genome: chromosome rearrangements by design. Genetics 1996, 144, 1693-1711. [55] Venken, K. J., Bellen, H. J., Emerging technologies for gene manipulation in Drosophila melanogaster. Nat Rev Genet 2005, 6, 167-178. [56] Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K., et al., From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology (N Y) 1996, 14, 61-65. [57] Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., Whitehouse, C. M., Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246, 64-71. [58] Hillenkamp, F., Karas, M., Beavis, R. C., Chait, B. T., Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers. Anal Chem 1991, 63, 1193A-1203A. [59] Washburn, M. P., Wolters, D., Yates, J. R., 3rd, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19, 242-247. [60] Wolters, D. A., Washburn, M. P., Yates, J. R., 3rd, An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 2001, 73, 5683-5690. [61] Marcotte, E. M., How do shotgun proteomics algorithms identify proteins? Nat Biotechnol 2007, 25, 755-757. [62] Jimmy K, Ashle L, John R. Yates, I., An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database J Am Soc Mass Spectrom 1994, 5, 976–989. [63] Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567. [64] Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467. [65] Geer, B. W., Utilization of D-amino acids for growth by Drosophila melanogaster larvae. J Nutr 1966, 90, 31-39. [66] Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res, 10, 1794-1805. [67] Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4, 207-214. [68] Elias, J. E., Gygi, S. P., Target-decoy search strategy for mass spectrometry-based proteomics. Methods Mol Biol, 604, 55-71. [69] Deutsch, E. W., Lam, H., Aebersold, R., Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 2008, 33, 18-25. [70] McLafferty, F. W., Breuker, K., Jin, M., Han, X., et al., Top-down MS, a powerful complement to the high capabilities of proteolysis proteomics. FEBS J 2007, 274, 6256-6268. [71] Cox, J., Mann, M., Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology. Annu Rev Biochem. [72] Chait, B. T., Chemistry. Mass spectrometry: bottom-up or top-down? Science 2006, 314, 65-66. [73] Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17, 994-999. [74] Oda, Y., Huang, K., Cross, F. R., Cowburn, D., Chait, B. T., Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci U S A 1999, 96, 6591-6596. [75] Pasa-Tolic L, Jensen PK, Anderson GA, Lipton MS, et al., High throughput proteome wide precision measurements of protein expression using mass spectrometry. J Am Chem Soc 1999, 121, 7949-7950. [76] Qiu, Y., Sousa, E. A., Hewick, R. M., Wang, J. H., Acid-labile isotope-coded extractants: a class of reagents for quantitative mass spectrometric analysis of complex protein mixtures. Anal Chem 2002, 74, 4969-4979. [77] Zhang, R., Sioma, C. S., Thompson, R. A., Xiong, L., Regnier, F. E., Controlling deuterium isotope effects in comparative proteomics. Anal Chem 2002, 74, 3662-3669. [78] Zhang, R., Regnier, F. E., Minimizing resolution of isotopically coded peptides in comparative proteomics. J Proteome Res 2002, 1, 139-147. [79] Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3, 1154-1169. [80] Thompson, A., Schafer, J., Kuhn, K., Kienle, S., et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75, 1895-1904. [81] Schmidt, A., Kellermann, J., Lottspeich, F., A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 2005, 5, 4-15. [82] Yao, X., Freas, A., Ramirez, J., Demirev, P. A., Fenselau, C., Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 2001, 73, 2836-2842. [83] Reynolds, K. J., Yao, X., Fenselau, C., Proteolytic 18O labeling for comparative proteomics: evaluation of endoprotease Glu-C as the catalytic agent. J Proteome Res 2002, 1, 27-33. [84] Ramos-Fernandez, A., Lopez-Ferrer, D., Vazquez, J., Improved method for differential expression proteomics using trypsin-catalyzed 18O labeling with a correction for labeling efficiency. Mol Cell Proteomics 2007, 6, 1274-1286. [85] Gouw, J. W., Krijgsveld, J., Heck, A. J., Quantitative proteomics by metabolic labeling of model organisms. Mol Cell Proteomics, 9, 11-24. [86] Dreisbach, A., Otto, A., Becher, D., Hammer, E., et al., Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques. Proteomics 2008, 8, 2062-2076. [87] Xia, Q., Hendrickson, E. L., Zhang, Y., Wang, T., et al., Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics 2006, 5, 868-881. [88] Lanquar, V., Kuhn, L., Lelievre, F., Khafif, M., et al., 15N-metabolic labeling for comparative plasma membrane proteomics in Arabidopsis cells. Proteomics 2007, 7, 750-754. [89] Gruhler, A., Schulze, W. X., Matthiesen, R., Mann, M., Jensen, O. N., Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol Cell Proteomics 2005, 4, 1697-1709. [90] Krijgsveld, J., Ketting, R. F., Mahmoudi, T., Johansen, J., et al., Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 2003, 21, 927-931. [91] Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., Yates, J. R., 3rd, Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem 2004, 76, 4951-4959. [92] Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1, 376-386. [93] Gu, S., Pan, S., Bradbury, E. M., Chen, X., Precise peptide sequencing and protein quantification in the human proteome through in vivo lysine-specific mass tagging. J Am Soc Mass Spectrom 2003, 14, 1-7. [94] Ishihama, Y., Sato, T., Tabata, T., Miyamoto, N., et al., Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat Biotechnol 2005, 23, 617-621. [95] Ong, S. E., Mittler, G., Mann, M., Identifying and quantifying in vivo methylation sites by heavy methyl SILAC. Nat Methods 2004, 1, 119-126. [96] Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., et al., A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol 2003, 21, 315-318. [97] Ong, S. E., Kratchmarova, I., Mann, M., Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res 2003, 2, 173-181. [98] Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26, 1367-1372. [99] Mann, M., Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 2006, 7, 952-958. [100] Gouw, J. W., Tops, B. B., Mortensen, P., Heck, A. J., Krijgsveld, J., Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomics. Anal Chem 2008, 80, 7796-7803. [101] Liao, L., Park, S. K., Xu, T., Vanderklish, P., Yates, J. R., 3rd, Quantitative proteomic analysis of primary neurons reveals diverse changes in synaptic protein content in fmr1 knockout mice. Proc Natl Acad Sci U S A 2008, 105, 15281-15286. [102] Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B., Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007, 389, 1017-1031. [103] Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., et al., Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 2005, 4, 1487-1502. [104] Bondarenko, P. V., Chelius, D., Shaler, T. A., Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal Chem 2002, 74, 4741-4749. [105] Ono, M., Shitashige, M., Honda, K., Isobe, T., et al., Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics 2006, 5, 1338-1347. [106] Wiener, M. C., Sachs, J. R., Deyanova, E. G., Yates, N. A., Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem 2004, 76, 6085-6096. [107] Wang, W., Zhou, H., Lin, H., Roy, S., et al., Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 2003, 75, 4818-4826. [108] Waanders, L. F., Chwalek, K., Monetti, M., Kumar, C., et al., Quantitative proteomic analysis of single pancreatic islets. Proc Natl Acad Sci U S A 2009, 106, 18902-18907. [109] Wang, Z., Udeshi, N. D., Slawson, C., Compton, P. D., et al., Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis. Sci Signal, 3, ra2. [110] Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., et al., Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 2009, 325, 834-840. [111] Kim, S. C., Sprung, R., Chen, Y., Xu, Y., et al., Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 2006, 23, 607-618. [112] Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., et al., A proteomics approach to understanding protein ubiquitination. Nat Biotechnol 2003, 21, 921-926. [113] Hitchcock, A. L., Auld, K., Gygi, S. P., Silver, P. A., A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery. Proc Natl Acad Sci U S A 2003, 100, 12735-12740. [114] Denison, C., Rudner, A. D., Gerber, S. A., Bakalarski, C. E., et al., A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol Cell Proteomics 2005, 4, 246-254. [115] Kaminsky, R., Denison, C., Bening-Abu-Shach, U., Chisholm, A. D., et al., SUMO regulates the assembly and function of a cytoplasmic intermediate filament protein in C. elegans. Dev Cell 2009, 17, 724-735. [116] Golebiowski, F., Matic, I., Tatham, M. H., Cole, C., et al., System-wide changes to SUMO modifications in response to heat shock. Sci Signal 2009, 2, ra24. [117] Macek, B., Mann, M., Olsen, J. V., Global and site-specific quantitative phosphoproteomics: principles and applications. Annu Rev Pharmacol Toxicol 2009, 49, 199-221. [118] Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., et al., Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A 2004, 101, 12130-12135. [119] Schroeder, M. J., Shabanowitz, J., Schwartz, J. C., Hunt, D. F., Coon, J. J., A neutral loss activation method for improved phosphopeptide sequence analysis by quadrupole ion trap mass spectrometry. Anal Chem 2004, 76, 3590-3598. [120] Zubarev, R. A., Horn, D. M., Fridriksson, E. K., Kelleher, N. L., et al., Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem 2000, 72, 563-573. [121] Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., Hunt, D. F., Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 2004, 101, 9528-9533. [122] Stensballe, A., Jensen, O. N., Olsen, J. V., Haselmann, K. F., Zubarev, R. A., Electron capture dissociation of singly and multiply phosphorylated peptides. Rapid Commun Mass Spectrom 2000, 14, 1793-1800. [123] Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J., et al., Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A 2007, 104, 2193-2198. [124] Good, D. M., Wirtala, M., McAlister, G. C., Coon, J. J., Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics 2007, 6, 1942-1951. [125] Swaney, D. L., McAlister, G. C., Coon, J. J., Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat Methods 2008, 5, 959-964. [126] Tsai, C. F., Wang, Y. T., Chen, Y. R., Lai, C. Y., et al., Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics. J Proteome Res 2008, 7, 4058-4069. [127] Andersson, L., Porath, J., Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. Anal Biochem 1986, 154, 250-254. [128] Posewitz, M. C., Tempst, P., Immobilized gallium(III) affinity chromatography of phosphopeptides. Anal Chem 1999, 71, 2883-2892. [129] Ndassa, Y. M., Orsi, C., Marto, J. A., Chen, S., Ross, M. M., Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications. J Proteome Res 2006, 5, 2789-2799. [130] Kokubu, M., Ishihama, Y., Sato, T., Nagasu, T., Oda, Y., Specificity of immobilized metal affinity-based IMAC/C18 tip enrichment of phosphopeptides for protein phosphorylation analysis. Anal Chem 2005, 77, 5144-5154. [131] Kim, J. E., Tannenbaum, S. R., White, F. M., Global phosphoproteome of HT-29 human colon adenocarcinoma cells. J Proteome Res 2005, 4, 1339-1346. [132] Villen, J., Gygi, S. P., The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat Protoc 2008, 3, 1630-1638. [133] Nuhse, T. S., Stensballe, A., Jensen, O. N., Peck, S. C., Large-scale analysis of in vivo phosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry. Mol Cell Proteomics 2003, 2, 1234-1243. [134] McNulty, D. E., Annan, R. S., Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol Cell Proteomics 2008, 7, 971-980. [135] Pinkse, M. W., Uitto, P. M., Hilhorst, M. J., Ooms, B., Heck, A. J., Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal Chem 2004, 76, 3935-3943. [136] Jensen, S. S., Larsen, M. R., Evaluation of the impact of some experimental procedures on different phosphopeptide enrichment techniques. Rapid Commun Mass Spectrom 2007, 21, 3635-3645. [137] Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., Jorgensen, T. J., Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol Cell Proteomics 2005, 4, 873-886. [138] Thingholm, T. E., Jorgensen, T. J., Jensen, O. N., Larsen, M. R., Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc 2006, 1, 1929-1935. [139] Bodenmiller, B., Mueller, L. N., Mueller, M., Domon, B., Aebersold, R., Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods 2007, 4, 231-237. [140] Thingholm, T. E., Jensen, O. N., Robinson, P. J., Larsen, M. R., SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics 2008, 7, 661-671. [141] Hunter, T., Sefton, B. M., Transforming gene product of Rous sarcoma virus phosphorylates tyrosine. Proc Natl Acad Sci U S A 1980, 77, 1311-1315. [142] Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648. [143] Hinsby, A. M., Olsen, J. V., Bennett, K. L., Mann, M., Signaling initiated by overexpression of the fibroblast growth factor receptor-1 investigated by mass spectrometry. Mol Cell Proteomics 2003, 2, 29-36. [144] Blagoev, B., Ong, S. E., Kratchmarova, I., Mann, M., Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 2004, 22, 1139-1145. [145] Olsen, J. V., Vermeulen, M., Santamaria, A., Kumar, C., et al., Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal, 3, ra3. [146] Rush, J., Moritz, A., Lee, K. A., Guo, A., et al., Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 2005, 23, 94-101. [147] Rikova, K., Guo, A., Zeng, Q., Possemato, A., et al., Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2007, 131, 1190-1203. [148] Ito, T., Chiba, T., Ozawa, R., Yoshida, M., et al., A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 2001, 98, 4569-4574. [149] Krogan, N. J., Cagney, G., Yu, H., Zhong, G., et al., Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440, 637-643. [150] Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., et al., Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415, 180-183. [151] Gavin, A. C., Aloy, P., Grandi, P., Krause, R., et al., Proteome survey reveals modularity of the yeast cell machinery. Nature 2006, 440, 631-636. [152] Gavin, A. C., Bosche, M., Krause, R., Grandi, P., et al., Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415, 141-147. [153] Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., et al., A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403, 623-627. [154] Formstecher, E., Aresta, S., Collura, V., Hamburger, A., et al., Protein interaction mapping: a Drosophila case study. Genome Res 2005, 15, 376-384. [155] Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., et al., A protein interaction map of Drosophila melanogaster. Science 2003, 302, 1727-1736. [156] Stanyon, C. A., Liu, G., Mangiola, B. A., Patel, N., et al., A Drosophila protein-interaction map centered on cell-cycle regulators. Genome Biol 2004, 5, R96. [157] Li, S., Armstrong, C. M., Bertin, N., Ge, H., et al., A map of the interactome network of the metazoan C. elegans. Science 2004, 303, 540-543. [158] Stelzl, U., Worm, U., Lalowski, M., Haenig, C., et al., A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005, 122, 957-968. [159] Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., et al., Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437, 1173-1178. [160] Gandhi, T. K., Zhong, J., Mathivanan, S., Karthick, L., et al., Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 2006, 38, 285-293. [161] Charbonnier, S., Gallego, O., Gavin, A. C., The social network of a cell: recent advances in interactome mapping. Biotechnol Annu Rev 2008, 14, 1-28. [162] von Mering, C., Krause, R., Snel, B., Cornell, M., et al., Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417, 399-403. [163] Puig, O., Caspary, F., Rigaut, G., Rutz, B., et al., The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 2001, 24, 218-229. [164] Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., et al., A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 1999, 17, 1030-1032. [165] Gingras, A. C., Gstaiger, M., Raught, B., Aebersold, R., Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 2007, 8, 645-654. [166] Gavin, A. C., Maeda, K., Kuhner, S., Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. Curr Opin Biotechnol, 22, 42-49. [167] Gingras, A. C., Aebersold, R., Raught, B., Advances in protein complex analysis using mass spectrometry. J Physiol 2005, 563, 11-21. [168] Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., et al., Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell, 142, 967-980. [169] Selbach, M., Mann, M., Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat Methods 2006, 3, 981-983. [170] Hubner, N. C., Mann, M., Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC). Methods, 53, 453-459. [171] Eberl, H. C., Mann, M., Vermeulen, M., Quantitative proteomics for epigenetics. Chembiochem, 12, 224-234. [172] Vermeulen, M., Hubner, N. C., Mann, M., High confidence determination of specific protein-protein interactions using quantitative mass spectrometry. Curr Opin Biotechnol 2008, 19, 331-337. [173] Makhnevych, T., Sydorskyy, Y., Xin, X., Srikumar, T., et al., Global map of SUMO function revealed by protein-protein interaction and genetic networks. Mol Cell 2009, | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/23898 | - |
dc.description.abstract | Abstract
To know the signaling pathways that protein tyrosine phosphatases (PTPs) are involved, it is important to identify the substrates of PTPs. However, prior strategies for identification of substrates of PTPs were suboptimal. Therefore establishment of a generic method for large scale screening of potential substrates of PTPs is necessary. In the first part of this thesis, substrate trapping was coupled with mass spectrometry to identify substrates of PTP61F, an ortholog of human PTP1B. The total lysate or enriched tyrosine proteins were used as input to perform substrate trapping. To reduce non specific associated proteins, which is the major cause of false positive identification, vanadate, a competitive inhibitor, was used to specifically elute the substrates from PTP-substrate complexes. More than 60 substrates were identified in our substrate trapping assay. The substrates identified in this study highlight a connection of PTP61F to cytosketal regulation through focal adhesion components. Subsequent genetic and biochemistry studies by others in our group have since demonstrated that several of the identified substrates are direct and physiological substrates in vivo. Moreover, this strategy has already been extended to other PTPs such as PTPmeg in Drosophila. The second part of this work aimed to develop a method to facilitate the quantitative analysis of multiple proteins in Drosophila in vivo. This quantitative strategy could be combined with other methods such as substrate trapping or RNAi interference to help us to investigate the functional PTPome. We have successfully established a viable SILAC fly approach for this aim. We showed that metabolic labeling with lysine was suboptimal for quantitative experiment in Drosophila in vivo because the conversion of heavy isotope labeled lysine to other unexpected amino acids affected quantitation accuracy. On the other hand, we have also investigated the alternative use of Arg10 in the applications of in vivo SILAC strategy. Although the conversion of arginine to other amino acid could be observed, the conversion rates seemed to be negligible except for proline. Thus upon a simple normalization of arginine to proline effcet, the systematic bias could be largely rectified. In our Arg0 to Arg10 1:1 test, 98% of protein ratios were within ±0.5, indicative of high accuracy. Additionally, we have also applied the SILAC flies using Arg10 labeling strategy for quantitative comparison of the expressed proteomes, between puparium formation and 3 h after puparium. Our data has shown similar changes in expression at the mRNA and protein levels. We have also successful used 5% SILAC yeast fly food to replace the diet with exclusive yeast. This makes SILAC flies inexpensive and more practical for quantitative experiments. Collectively we have established generic platforms incorporating shotgun and quantitative proteomic strategies to facilitate the study of functional PTPomics. | en |
dc.description.provenance | Made available in DSpace on 2021-06-08T05:12:13Z (GMT). No. of bitstreams: 1 ntu-100-D94b46012-1.pdf: 2839144 bytes, checksum: c2700f5437b47f38f11d54d481a37598 (MD5) Previous issue date: 2011 | en |
dc.description.tableofcontents | 中文摘要 I
Abstract II Chapter1 Introduction 1 1.1 Protein tyrosine phosphatase 1 1.1.1 Substrate trapping assay 2 1.1.2 The basic catalysis mechanism of classical PTPs 2 1.1.3 Substrate trapping mutant 2 1.1.4 Drosophila melanogaster as a model organism to study the functions of PTPs 3 1.2 Mass spectrometry based proteomics 4 1.2.1 Shotgun proteomics 5 1.3 Quantitative proteomics 6 1.3.1 Label-based quantitative proteomics 6 1.3.2 Label-free quantitative proteomics 8 1.4 Post translational modifications (PTM) 8 1.4.1 Phosphoproteomics 9 1.4.2 Phosphopeptide enrichment strategies 10 1.4.2.1 Immobilized Metal Affinity Chromatography (IMAC) 10 1.4.2.2 Titanium Dioxide Enrichment 10 1.4.3.3 Antibody-Based Enrichment 11 1.5 Protein interaction (interactome) 11 1.6 Overview and Aims of this thesis 12 Chater 2 Phosphotyrosine proteome and substrate trapping assay using mass spectromtery 14 2.1 Brief introduction 14 2.2 Material and Method 14 2.2.1 Plasmid constructs and purification of recombinant PTP61F 14 2.2.2 Cell culture and lysate preparation 14 2.2.3 Affinity purification of pTyr proteome subset 15 2.2.4 Trypsin digestion of pTyr proteins and enrichment of pTyr peptides 15 2.2.5 Direct substrate trapping experiments 16 2.2.6 Indirect substrate trapping experiments 16 2.2.7 Mass spectrometric analysis 16 2.2.8 Data analysis 17 2.3 Results 18 2.3.1 Profiling of pTyr proteome in S2 cells by mass spectrometry 18 2.3.2 Construction of PTP61F-D/A mutant for substrate trapping experiments 19 2.3.3 Identification of substrates of PTP61F from S2 lysates by mass spectrometry 19 2.3.4 Identification of substrates of PTP61F from enriched pTyr proteome subset of S2 cells by mass spectrometry 20 2.4 Discussion 20 2.5 Figures and tables 24 Chapter 3 SILAC fly for quantitative experiments 40 3.1 Brief introduction 40 3.2 Material and method 41 3.2.1 SILAC fly food preparation 41 3.2.2 SILAC fly labeling and sample preparation 41 3.2.3 In-gel digestion 41 3.2.4 Mass spectrometric analysis 42 3.2.5 Data analysis and quantification 42 3.3 Results 43 3.3.1 D. melanogaster labeled with heavy lysine 43 3.3.2 The isotope distribution patterns in Lys8 labeled peptides were changed 43 3.3.3 The Lys8 to Lys0 ratios were underestimated in Drosophila 44 3.3.4 The bias of underestimation was due to conversion of Lys8 to numerous non-essential amino acids 44 3.3.5 Labeling with heavy arginine allows for precise protein quantification 46 3.3.6 Quantitative proteomics of D.melanogaster in vivo between and after puparium 47 3.4 Discussions 48 3.5 Figures and tables 51 Chapter 4 Conclusion and Perspectives 70 Chater 5 References 74 | |
dc.language.iso | en | |
dc.title | 以蛋白質體學技術研究果蠅酪氨酸磷酸化及酪氨酸磷酸水解脢之受質 | zh_TW |
dc.title | Strategies and enabling proteomic techniques for the studies of protein tyrosine phosphatase and its substrates in Drosophila | en |
dc.type | Thesis | |
dc.date.schoolyear | 99-2 | |
dc.description.degree | 博士 | |
dc.contributor.coadvisor | 孟子青 | |
dc.contributor.oralexamcommittee | 張震東,陳光超,簡正鼎 | |
dc.subject.keyword | 果蠅, | zh_TW |
dc.subject.keyword | SILAC,Drosophila, | en |
dc.relation.page | 87 | |
dc.rights.note | 未授權 | |
dc.date.accepted | 2011-08-02 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 生化科學研究所 | zh_TW |
顯示於系所單位: | 生化科學研究所 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-100-1.pdf 目前未授權公開取用 | 2.77 MB | Adobe PDF |
系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。